Advertisement

Amino Acids

, Volume 33, Issue 1, pp 113–121 | Cite as

Multi-layered network structure of amino acid (AA) metabolism characterized by each essential AA-deficient condition

  • N. Shikata
  • Y. Maki
  • Y. Noguchi
  • M. Mori
  • T. Hanai
  • M. Takahashi
  • M. Okamoto
Article

Summary.

The concentrations of free amino acids in plasma change coordinately and their profiles show distinctive features in various physiological conditions; however, their behavior can not always be explained by the conventional flow-based metabolic pathway network. In this study, we have revealed the interrelatedness of the plasma amino acids and inferred their network structure with threshold-test analysis and multilevel-digraph analysis methods using the plasma samples of rats which are fed diet deficient in single essential amino acid.

In the inferred network, we could draw some interesting interrelations between plasma amino acids as follows: 1) Lysine is located at the top control level and has effects on almost all of the other plasma amino acids. 2) Threonine plays a role in a hub in the network, which has direct links to the most number of other amino acids. 3) Threonine and methionine are interrelated to each other and form a loop structure.

Keywords: Plasma amino acids – Profile – Relation – Network – Threonine – Amino acid deficiency 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Allen, RH, Stabler, SP, Savage, DG, Lindenbaum, J 1993Metabolic abnormalities in cobalamin (vitamin B12) and folate deficiencyFaseb J713441353PubMedGoogle Scholar
  2. Althaus, IW, Chou, JJ, Gonzales, AJ, Deibel, MR, Chou, KC, Kezdy, FJ, Romero, DL, Aristoff, PA, Tarpley, WG, Reusser, F 1993aSteady-state kinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-87201EJ Biol Chem26861196124Google Scholar
  3. Althaus, IW, Chou, JJ, Gonzales, AJ, Deibel, MR, Chou, KC, Kezdy, FJ, Romero, DL, Palmer, JR, Thomas, RC, Aristoff, PA,  et al. 1993bKinetic studies with the non-nucleoside HIV-1 reverse transcriptase inhibitor U-88204EBiochemistry3265486554CrossRefGoogle Scholar
  4. Althaus, IW, Gonzales, AJ, Chou, JJ, Romero, DL, Deibel, MR, Chou, KC, Kezdy, FJ, Resnick, L, Busso, ME, So, AG,  et al. 1993cThe quinoline U-78036 is a potent inhibitor of HIV-1 reverse transcriptaseJ Biol Chem2681487514880Google Scholar
  5. Banerjee, R, Zou, CG 2005Redox regulation and reaction mechanism of human cystathionine-beta-synthase: a PLP-dependent hemesensor proteinArch Biochem Biophys433144156PubMedCrossRefGoogle Scholar
  6. Borcsok, E, Abeles, RH 1982Mechanism of action of cystathionine synthaseArch Biochem Biophys213695707PubMedCrossRefGoogle Scholar
  7. Chou, KC 1981Two new schematic rules for rate laws of enzyme-catalysed reactionsJ Theor Biol89581592PubMedCrossRefGoogle Scholar
  8. Chou, KC 1989Graphic rules in steady and non-steady state enzyme kineticsJ Biol Chem2641207412079PubMedGoogle Scholar
  9. Chou, KC 1990Applications of graph theory to enzyme kinetics and protein folding kinetics. Steady and non-steady-state systemsBiophys Chem35124PubMedCrossRefGoogle Scholar
  10. Chou, KC, Liu, WM 1981Graphical rules for non-steady state enzyme kineticsJ Theor Biol91637654CrossRefGoogle Scholar
  11. Chou, KC, Kezdy, FJ, Reusser, F 1994Kinetics of processive nucleic acid polymerases and nucleasesAnal Biochem221217PubMedCrossRefGoogle Scholar
  12. Chou, KC, Cai, YD, Zhong, WZ 2006Predicting networking couples for metabolic pathways of ArabidopsisEXCLI J55565Google Scholar
  13. Felig, P 1975Amino acid metabolism in manAnnu Rev Biochem44933955PubMedCrossRefGoogle Scholar
  14. Ferenci, P, Wewalka, F 1978Plasma amino acids in hepatic encephalopathyJ Neural Transm [Suppl]148794Google Scholar
  15. Holm, E, Sedlaczek, O, Grips, E 1999Amino acid metabolism in liver diseaseCurr Opin Clin Nutr Metab Care24753PubMedCrossRefGoogle Scholar
  16. Hong, SY, Yang, DH, Chang, SK 1998The relationship between plasma homocysteine and amino acid concentrations in patients with end-stage renal diseaseJ Ren Nutr83439PubMedGoogle Scholar
  17. Jimenez Jimenez, FJ, Ortiz Leyba, C, Morales Menedez, S, Barros Perez, M, Munoz Garcia, J 1991Prospective study on the efficacy of branched-chain amino acids in septic patientsJPEN15252261Google Scholar
  18. Kadowaki, M, Kanazawa, T 2003Amino acids as regulators of proteolysisJ Nutr1332052S2056SPubMedGoogle Scholar
  19. Kapke, G, Davis, L 1976Stereochemistry of the reaction of sheep liver threonine dehydratase. A nuclear magnetic resonance and optical rotatory dispersion study of its reaction pathway and productsBiochemistry1537453749PubMedCrossRefGoogle Scholar
  20. Kimball, SR 2002Regulation of global and specific mRNA translation by amino acidsJ Nutr132883886PubMedGoogle Scholar
  21. Kuzmic, P, Ng, KY, Heath, TD 1992Mixtures of tight-binding enzyme inhibitors. Kinetic analysis by a recursive rate equationAnal Biochem2006873PubMedCrossRefGoogle Scholar
  22. Lin, SX, Neet, KE 1990Demonstration of a slow conformational change in liver glucokinase by fluorescence spectroscopyJ Biol Chem26596709675PubMedGoogle Scholar
  23. Maki, Y, Takahashi, Y, Arikawa, Y, Watanabe, S, Aoshima, K, Eguchi, Y, Ueda, T, Aburatani, S, Kuhara, S, Okamoto, M 2004An integrated comprehensive workbench for inferring genetic networks: voyageneJ Bioinform Comput Biol2533550PubMedCrossRefGoogle Scholar
  24. Maki, Y, Tominaga, D, Okamoto, M, Watanabe, S, Eguchi, Y 2001Development of a system for the inference of large scale genetic networksPac Symp Biocomput6446458Google Scholar
  25. Nicholson, JK, Lindon, JC, Holmes, E 1999‘Metabonomics’: understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic dataXenobiotica2911811189PubMedCrossRefGoogle Scholar
  26. Noguchi, Y, Zhang, QW, Sugimoto, T, Furuhata, Y, Sakai, R, Mori, M, Takahashi, M, Kimura, T 2006Network analysis of plasma and tissue amino acids and the generation of an amino index for potential diagnostic useAm J Clin Nutr83513S519SPubMedGoogle Scholar
  27. Scarselli, M, Padula, MG, Bernini, A, Spiga, O, Ciutti, A, Leoncini, R, Vannoni, D, Marinello, E, Niccolai, N 2003Structure and function correlations between the rat liver threonine deaminase and aminotransferasesBiochim Biophys Acta16454048PubMedGoogle Scholar
  28. Soeters, PB, Fischer, JE 1976Insulin, glucagon, aminoacid imbalance, and hepatic encephalopathyLancet2880882PubMedCrossRefGoogle Scholar
  29. Stabler, SP, Lindenbaum, J, Savage, DG, Allen, RH 1993Elevation of serum cystathionine levels in patients with cobalamin and folate deficiencyBlood8134043413PubMedGoogle Scholar
  30. Tudor, I, Tanase-Mogos, I, Tanasie, E, Badescu, E, Rascanu, M 1976A study of aminoacidemia and aminoaciduria in epileptic childrenNeurol Psychiatr (Bucur)14277282Google Scholar
  31. Wang, M, Yao, JS, Huang, ZD, Xu, ZJ, Liu, GP, Zhao, HY, Wang, XY, Yang, J, Zhu, YS, Chou, KC 2005A new nucleotide-composition based fingerprint of SARS-CoV with visualization analysisMed Chem13947PubMedCrossRefGoogle Scholar
  32. Watanabe, A, Higashi, T, Sakata, T, Nagashima, H 1984Serum amino acid levels in patients with hepatocellular carcinomaCancer5418751882PubMedCrossRefGoogle Scholar
  33. Watanabe, A, Takei, N, Hayashi, S, Nagashima, H 1983Serum neutral amino acid concentrations in cirrhotic patients with impaired carbohydrate metabolismActa Med Okayama37381384PubMedGoogle Scholar
  34. Watanabe, F, Nakano, Y 1999[Vitamin B12]Nippon Rinsho5722052210PubMedGoogle Scholar
  35. Xiao, X, Shao, S, Ding, Y, Huang, Z, Chen, X, Chou, KC 2005aAn application of gene comparative image for predicting the effect on replication ratio by HBV virus gene missense mutationJ Theor Biol235555565CrossRefGoogle Scholar
  36. Xiao, X, Shao, S, Ding, Y, Huang, Z, Chen, X, Chou, KC 2005bUsing cellular automata to generate image representation for biological sequencesAmino Acids282935CrossRefGoogle Scholar
  37. Xiao, X, Shao, S, Ding, Y, Huang, Z, Chou, KC 2006aUsing cellular automata images and pseudo amino acid composition to predict protein subcellular locationAmino Acids304954CrossRefGoogle Scholar
  38. Xiao, X, Shao, SH, Chou, KC 2006bA probability cellular automaton model for hepatitis B viral infectionsBiochem Biophys Res Commun342605610CrossRefGoogle Scholar
  39. Yeang, CH, Mak, HC, McCuine, S, Workman, C, Jaakkola, T, Ideker, T 2005Validation and refinement of gene-regulatory pathways on a network of physical interactionsGenome Biol6R62PubMedCrossRefGoogle Scholar
  40. Zhang, CT, Chou, KC 1996An analysis of base frequencies in the anti-sense strands corresponding to the 180 human protein coding sequencesAmino Acids10253262CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • N. Shikata
    • 1
  • Y. Maki
    • 2
  • Y. Noguchi
    • 3
  • M. Mori
    • 3
  • T. Hanai
    • 1
  • M. Takahashi
    • 3
  • M. Okamoto
    • 1
  1. 1.Graduate School of Systems Life SciencesKyushu UniversityFukuokaJapan
  2. 2.Department of Digital MediaFukuoka International UniversityFukuokaJapan
  3. 3.Research Institute for Health FundamentalsAjinomoto Co., Inc.KawasakiJapan

Personalised recommendations